Tomato quality is intricately regulated by a combination of factors, including the presence of bioactive compounds referred to as secondary metabolites and various organoleptic characteristics. These attributes are notably influenced and harmonized by the specific growing conditions, with a particular emphasis on the type of fertilization employed. Traditionally, chemical fertilizers have been favored in crop cultivation due to their cost-effectiveness and ability to accelerate crop growth. However, in pursuit of sustainable and intelligent agricultural practices, there is a growing need for alternative fertilizers. In this context, the present study aimed to assess the impact of fertilizers derived from waste materials, specifically sulfur bentonite and orange residue (referred to as SB), on tomato quality. This assessment extended to examining qualitative and quantitative alterations in aroma-related volatile compounds and the antioxidant systems of tomatoes, in comparison to the conventional use of fertilizers such as horse manure (HM) and nitrogen, phosphorus, and potassium (NPK). The results obtained revealed distinct effects of different fertilizers on tomato quality. Notably, parameters such as TPRO (total protein), TCARB (total carbohydrate), LIC (lycopene content), TCAR (total carotenoid content), total phenols (TPHE), total flavonoids (TFLA), and aroma profiling exhibited significantly superior values in the group treated with sulfur bentonite (SB) fertilizer. These findings strongly suggest that the novel fertilizer functioned as a biostimulant, enhancing the nutraceutical and sensory attributes of tomatoes, with a pronounced impact on the synthesis of secondary metabolites and the aroma profile of the fruits.